The 72-year-old singer-songwriter, who has performed with Pink Floyd and was cited as an influence by Led Zeppelin, was not required to enter a plea to any of the charges.
Harper, who lives in Ireland, is accused of two counts of having unlawful sexual intercourse with a girl aged under 13.
The singer also faces three charges of indecent assault and four of gross indecency relating to the same alleged victim.
Harper, who has made more than 30 albums and continues to tour, appeared at Hereford Magistrates' Court in central England.
Harper, dressed casually in a checked shirt and blue jeans, spoke only to give his name and address. He declined to comment to reporters afterwards.
He was granted unconditional bail and ordered to appear before a judge at Worcester Crown Court on December 2.